Mitochondria are the convergence point of multiple pathways that trigger programmed cell death(PCD).Mitochondrial-associated PCD(mtPCD)is involved in the pathogenesis of several diseases.However,the role of mtPCD in t...Mitochondria are the convergence point of multiple pathways that trigger programmed cell death(PCD).Mitochondrial-associated PCD(mtPCD)is involved in the pathogenesis of several diseases.However,the role of mtPCD in the prognostic prediction of cancers including non-small-cell lung cancer(NSCLC)remains to be investigated.Here,12 mtPCD patterns were analyzed in transcriptomics,genomics,and clinical data collected from 4 datasets containing 977 patients.A risk-score assessment system containing 18 genes was established.We found that NSCLC patients with a high-risk score had a poorer prognosis.A nomogram was constructed by incorporating the risk score with clinical features.The risk score was further associated with clinicopathological information,tumor-mutation frequency,and immunotherapy responses.NSCLC patients with a high risk score had more Treg cells infiltration.However,these patients had higher tumor-mutation burden scores and may be more sensitive to immunotherapy.Moreover,receptor-interacting serine/threonine protein kinase 2(RIPK2)was selected from mtPCD gene model for validation.We found that RIPK2 exhibited oncogenic function,and its expression level was inversely associated with the overall survival of NSCLC.Taken together,our results indicated the accuracy and practicability of the mtPCD gene model and RIPK2 in predicting the prognosis of NSCLC.展开更多
Cellular indexing of transcriptomes and epitopes by sequencing(CITE-seq)enables the simultaneous analysis of transcriptomic and proteomic data at the single-cell level,providing a comprehensive view of cellular hetero...Cellular indexing of transcriptomes and epitopes by sequencing(CITE-seq)enables the simultaneous analysis of transcriptomic and proteomic data at the single-cell level,providing a comprehensive view of cellular heterogeneity and function.In this study,we present a standardized approach for high-quality single-cell RNA sequencing coupled with cell surface protein quantification.Key advantages of CITE-seq include its compatibility with existing scRNA-seq workflows,cost-efficient high-throughput protein detection,and enhanced resolution in cell type classification.Detailed steps for sample preparation,antibody-oligo conjugation,gel bead-in-emulsion(GEM)generation,complementary deoxyribonucleic acid(cDNA)amplification,and library construction are provided,ensuring reproducibility and robust data quality.This protocol facilitates the integration of multimodal single-cell data,enabling precise characterization of rare cell subsets and advancing insights in immunology,oncology,and developmental biology.The workflow is optimized for flexibility across platforms and scalable for diverse research applications.展开更多
基金supported by the National Key Research and Development Program of China(Nos.2023YFC3503205 and 2022YFA1103900)the CAMS Innovation Fund for Medical Sciences(CIFMS,No.2022-I2M-1-009)+3 种基金the National Natural Science Foundation of China(Nos.22372944,22073092 nnd 82273076)the Science and Technology Research Project of Henan Province(No.222122316366)the Henan Provincial Medical Science and Technology Research Project(No.LHGJ20210183)the Scientific Research Fund Project of the Affiliated Cancer Hospital of Zhengzhou University&Henan Cancer Hospital.
文摘Mitochondria are the convergence point of multiple pathways that trigger programmed cell death(PCD).Mitochondrial-associated PCD(mtPCD)is involved in the pathogenesis of several diseases.However,the role of mtPCD in the prognostic prediction of cancers including non-small-cell lung cancer(NSCLC)remains to be investigated.Here,12 mtPCD patterns were analyzed in transcriptomics,genomics,and clinical data collected from 4 datasets containing 977 patients.A risk-score assessment system containing 18 genes was established.We found that NSCLC patients with a high-risk score had a poorer prognosis.A nomogram was constructed by incorporating the risk score with clinical features.The risk score was further associated with clinicopathological information,tumor-mutation frequency,and immunotherapy responses.NSCLC patients with a high risk score had more Treg cells infiltration.However,these patients had higher tumor-mutation burden scores and may be more sensitive to immunotherapy.Moreover,receptor-interacting serine/threonine protein kinase 2(RIPK2)was selected from mtPCD gene model for validation.We found that RIPK2 exhibited oncogenic function,and its expression level was inversely associated with the overall survival of NSCLC.Taken together,our results indicated the accuracy and practicability of the mtPCD gene model and RIPK2 in predicting the prognosis of NSCLC.
基金supported by the Chinese Academy of Medical Sciences(CAMS)Innovation Funds for Medical Sciences(2024-I2M-3-001).
文摘Cellular indexing of transcriptomes and epitopes by sequencing(CITE-seq)enables the simultaneous analysis of transcriptomic and proteomic data at the single-cell level,providing a comprehensive view of cellular heterogeneity and function.In this study,we present a standardized approach for high-quality single-cell RNA sequencing coupled with cell surface protein quantification.Key advantages of CITE-seq include its compatibility with existing scRNA-seq workflows,cost-efficient high-throughput protein detection,and enhanced resolution in cell type classification.Detailed steps for sample preparation,antibody-oligo conjugation,gel bead-in-emulsion(GEM)generation,complementary deoxyribonucleic acid(cDNA)amplification,and library construction are provided,ensuring reproducibility and robust data quality.This protocol facilitates the integration of multimodal single-cell data,enabling precise characterization of rare cell subsets and advancing insights in immunology,oncology,and developmental biology.The workflow is optimized for flexibility across platforms and scalable for diverse research applications.
